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Right now my graphics card is in a PCI Express 3.0 x16 slot. Below that I have another PCI Express slot. The manual describes it as: "PCI Express 2.0 x16 slot (black at x4 mode, compatible with PCIe x1 and x4 devies [sic])." I want to put the add-on card into this slot. The add-on cards I'm looking at are all x1.

I've read that using multiple PCI Express slots can negatively impact the performance of other components in other PCI Express slots. How do I know if this is going to happen? Will installing this USB add-on card in the PCI Express 2.0 x16 slot decrease the performance of my graphics card in the PCI Express 3.0 x16 slot above it by forcing it to use less lanes and therefore run at a lower speed? Once I have it installed is there some way to test and find out if the graphics card's x16 slot is currently running at x1, x4, x8, or x16?

Also, I see that most of these cards come with a 5V 4-Pin power connector. Is this necessary if I'm hooking up devices that their own power supplies (like external hard drives with their own power cords)? Does using the power connector have any impact on the card's speed or other capabilities?

One final question, as far as I can tell all of these USB 3.0 add-on cards are made for PCI Express 1x slots. Is there a reason for this? Couldn't multiple USB 3.0 ports move enough data to bump into the PCI Express 2.0 x1 limit? Wouldn't a card with 4 USB 3.0 ports benefit from PCI Express 2.0 x4, x8, or x16?

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The manual suggests that using the second PCIe x16 slot will not affect the speed of the main (blue) PCIe slot (page 2-13).

Your motherboard also has PCIe x1 slots which you can use if you want (one of them may be blocked by the GPU cooler, the other should be accessible).

USB bandwidth is shared per hub/controller, so if you add a single 4 port USB 3.0 card, this will likely count as a single hub. Therefore, the maximum bandwidth available to all the ports combined will be 4 Gigabits per second, which is about the limit of a x1 PCIe 2.0 slot.

The manual suggests that using the second PCIe x16 slot will not affect the speed of the main (blue) PCIe slot (page 2-13).

OK, I see that chart now, and that seems to make sense. I'm just confused because on the motherboard's main ASUS page, when describing the board's features, it seems to imply that the PCIe 3.0 and 2.0 slots share the same lanes. Here's what it says:

That makes it sound like all the PCIe 3.0 and 2.0 slots are shared. Was it just poorly worded?

Your motherboard also has PCIe x1 slots which you can use if you want (one of them may be blocked by the GPU cooler, the other should be accessible).

Yeah, the lower PCIe x1 slot is covered by the graphics card. The top one should have been open, but the fan cooling the CPU is just large enough to block the top PCIe x1 port as well. (Definitely an annoying quirk, I didn't build the system.) I suppose I could replace the fan, but using the PCIe x16 slot seems like the better option given that it's not doing anything else at the moment.

My understanding is that the CPU has a 16 lane PCIe controller built in (in certain Ivy Bridge CPU's it is PCIe 3.0, otherwise PCIe 2.0) for the graphics, and there are a secondary 8 lanes of PCIe 2.0 provided by the Z77 chipset. This diagram may help.

I guess therefore that in that motherboard, the 16x lanes to the CPU are basically fixed to the main (blue) PCIe x16 slot. Intel do refer to the ability to split the CPU's PCIe lanes to an 8/8 or 8/4/4 configuration. However as the manual states that the secondary (black) x16 slot specifically is x4 PCIe 2.0, this suggests that it's using the chipset provided PCIe 2.0 lanes, rather than sharing the CPU's PCIe 2.0/3.0 lanes.

That's an assumption rather than a fact, but it is what the diagram above, combined with what the manual is stating suggests to me.

If the PCIe x1 ports are both blocked then of course it's fine to use the unused x16 slot, it should work without issue.